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ReadTheDocs updates for HEMCO 3.10.0 #292

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ReadTheDocs updates for HEMCO 3.10.0 #292

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@yantosca yantosca commented Oct 2, 2024

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Name: Bob Yantosca
Institution: Harvard + GCST

Describe the update

This PR seeks to merge documentation updates for HEMCO 3.10.0 into the dev/3.10.0 branch. We have made the following general updates:

  • Moved documentation for geoschem_config.yml, HEMCO_Diagn.rc, HEMCO_Config.rc, species_database.yml, and the aerosol/chemistry/photolysis configuration files to the https://github.com/geoschem/geos-chem-shared-docs repo.
  • Now point to relocated documentation files in the geos-chem-shared-docs repo
  • Added usage differences between GCHP and GCC for the various documentation files
  • Updated formatting to improve the page rendering and usability (i.e. using .. option:: tags, etc)

Related Github Issue

NOTES

For now I will leave this as a draft PR as we will might have more minor updates to push. But feel free to make comments & request changes on this PR now. Tagging @msulprizio @lizziel @yidant

docs/source/hco-ref-guide/more-examples.txt
- Removed the "Scale (or zero) emissions with a rectangular mask" example
  from the "More configuration examples" chapter.  @msulprizio pointed
  out in issue #286 that applying a scale factor to a mask does not
  currently work, and so this example also does not work properly.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>
docs/source/geos-chem-shared-docs
- Updated GNU 10.2.0 -> GNU 12.2.0 in Spack guide

docs/source/hco-sa-guide/login-env.rst
- Update environment file sample + text for GNU 12.2.0 compilers

docs/source/hco-sa-guide/software.rst
- The "skip ahead" link now poionts to the "Download the source code"
  chapter.

runHEMCO.sh
- Now pipe output to log file
- Also updated default SLURM partitions

Signed-off-by: Bob Yantosca <[email protected]>
This commit informs the HEMCO superproject about the following
commits pushed to the geos-chem-shared-docs submodule:

a68981b Update [email protected] -> [email protected] in load-libraries-guide.rst

This updates the GCC compiler version from 10.2.0 to 12.2.0 in the
various documentation pages.

Signed-off-by: Bob Yantosca <[email protected]>
docs/requirements.txt
- Use jinja 3.1.4 as there is a dependabot security warning for
  the previous version 3.1.3.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>
This commit informs the HEMCO superproject about the following
commits that were pushed to the GitHub geos-chem-shared-docs repo:

8ed145c Fixed typo in doc/geoschem-config.rst
9c7903d Add GCHP vs. GCC usage differences in HEMCO_Diagn.rc doc
b5420bb Add info about usage differences between GCHP & GCC
679cf4c Update geoschem-config.rst and phot-chem.rst
7a3e9db Created doc folder for common docs (not supplemental-guides)

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca yantosca added TODO: Documentation Improvements or additions to documentation no-diff-to-benchmark This update will have no impact on benchmark simulations labels Oct 2, 2024
@yantosca yantosca added this to the 3.10.0 milestone Oct 2, 2024
@yantosca yantosca self-assigned this Oct 2, 2024
This commit informs the HEMCO superproject about the following
commits that were pushed to the geos-chem-shared-docs repository:

65b2a35 Merge "docs/update_guides_for_gchp" into "main"
7f0cfbb Merge PR #3 (Add doc/tutorial for GEOS-Chem input data on AWS)

These are documentation updates for the GEOS-Chem 14.5.0 release.

Signed-off-by: Bob Yantosca <[email protected]>
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